Developmental Transcriptomes of S. purpuratus

What's New

2/2014 Important Notice: Some institution networks block traffic on port 2000. To ensure accessibility, the RNA-seq data web application has been moved to port 3838: http://www.echinobase.org:3838/quantdev/ Please update your bookmark. Sorry for the inconvenience.

1/2014: The paper describing the quantitative developmental transcriptomes is published on Developmental Biology.

11/2013: A completely new query tool, together with quantitative embryonic dataset, is released.

10/2012: The paper describing the gene structure is published on Genome Research.

6/2012: The quantitative expression data (FPKM) is now calculated from the CDS instead of the full-length sequence.

Introduction

In total 784 million 76bp pair-end reads were obtained. The reads were mapped onto the S. purpuratus genome v3.0, and new gene models were constructed. These RNA-seq models are identified with WHL22 prefix. Various information about the analysis is provided on this page.

The analysis was done based on S. purpuratus genome v3.0. The genome v3.0 differs with the current v3.1 in only a few places due to the removal of contaminating microbial sequences. The assembled transcript sequences remain the same, although the coordinates of exons might change.

The Search box accepts multiple ID/names. WHL and SPU IDs can be embedded in other text, and the program recognizes them by the pattern.Names have to be one name per line.

The expression cluster IDs can be found in this plot. They are [three-digit numbers] in the plot titles. Use the complete IDs like '020', not just '20'.

To use the IGV link, make sure you have downloaded the IGV program and it is running on your computer. The link will locate the corresponding gene model in the genome context.

mRNA sequences are sequences assembled directly from the RNA-seq data.CDS/protein sequences are predicted.

2. Gene Structure and Raw Reads, Using IGV Genome Browser

IGV (Integrative Genomics Viewer), developed by Broad Institute MIT, is a high-performance desktop genome browser for interactive exploration of large, integrated datasets. The genome view of RNA-seq models assembled in this study and reads etc can be accessed through IGV using the data server described below.

Quick Start:

Download IGV:

Go to IGV home page,download the program with the option for the maximum memory compatible with your computer, launch IGV. In practice, ~1G memory is necessary to load gene models, ~1.5-2G or even more memory is necessary to load reads.

Load the S. purpuratus genome:

In IGV, go to the genomes drop-down menu, select "S.purpuratus(3.0)", to load the scaffolds and GLEAN3 models.